The house fly Musca domestica L. (Diptera: Muscidae) is a worldwide medical and veterinary pest, causing great economic losses. Organophosphate insecticides have been widely used to control house fly populations. The main objectives of the present study were to evaluate the resistance levels of M. domestica slaughterhouse populations, collected from Riyadh, Jeddah, and Taif, against the organophosphate insecticide pirimiphos-methyl and investigate the genetic mutations of the Ace gene associated with pirimiphos-methyl resistance. The obtained data showed that there were significant differences among pirimiphos-methyl LC50 values of the studied populations, where the highest LC50 was recorded for the Riyadh population (8.44 mM), followed by Jeddah and Taif populations (2.45 mM and 1.63 mM, respectively). Seven nonsynonymous SNPs were detected in the studied house flies. The Ile239Val and Glu243Lys mutations are reported for the first time, whereas Val260Leu, Ala316Ser, Gly342Ala, Gly342Val, and Phe407Tyr were previously reported in M. domestica field populations from other countries. Considering three mutations associated with insecticide resistance, at amino acid positions 260, 342, and 407 of acetylcholinesterase polypeptide, 17 combinations were recovered in this study. Three out of these seventeen combinations were frequently found both worldwide and in the three Saudi house fly field populations, as well as their pirimiphos-methyl-surviving flies. Overall, the single and combined Ace mutations are apparently associated with pirimiphos-methyl resistance, and the obtained data can be useful in managing house fly field populations in Saudi Arabia.